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PDBsum entry 1ff5
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Cell adhesion
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PDB id
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1ff5
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Contents |
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* Residue conservation analysis
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DOI no:
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EMBO J
18:1738-1747
(1999)
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PubMed id:
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A new crystal structure, Ca2+ dependence and mutational analysis reveal molecular details of E-cadherin homoassociation.
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O.Pertz,
D.Bozic,
A.W.Koch,
C.Fauser,
A.Brancaccio,
J.Engel.
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ABSTRACT
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Electron microscopy of ECADCOMP, a recombinant E-cadherin ectodomain
pentamerized by the assembly domain of cartilage oligomeric matrix protein, has
been used to analyze the role of cis-dimerization and trans-interaction in the
homophilic association of this cell adhesion molecule. The Ca2+ dependency of
both interactions was investigated. Low Ca2+ concentrations (50 microM)
stabilized the rod-like structure of E-cadherin. At medium Ca2+ concentration
(500 microM), two adjacent ectodomains in a pentamer formed cis-dimers. At high
Ca2+ concentration (>1 mM), two cis-dimers from different pentamers formed a
trans-interaction. The X-ray structure of an N-terminal domain pair of
E-cadherin revealed two molecules per asymmetric unit in an intertwisted
X-shaped arrangement with closest contacts in the Ca2+-binding region between
domains 1 and 2. Contrary to previous data, Trp2 was docked in the hydrophobic
cavity of its own molecule, and was therefore not involved in cis-dimerization
of two molecules. This was supported further by W2A and A80I (a residue involved
in the hydrophobic cavity surrounding Trp2) mutations in ECADCOMP which both led
to abrogation of the trans- but not the cis-interaction. Structural and
biochemical data suggest a link between Ca2+ binding in the millimolar range and
Trp2 docking, both events being essential for the trans-association.
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Selected figure(s)
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Figure 4.
Figure 4 Final 2F[o]-F[c] stereoplot at a 1  contour
level of a region showing the hydrophobic cavity with (A) the
 A-strand
as in the M-ECAD12 structure and (B) the free tryptophan as in
the M-ECAD12+W structure. Continuous density (green) is observed
for the A-strand
(red), with chain tracing being unambiguous (A), whereas it
could only be traced from Ile4 in (B); additional density in the
hydrophobic pocket was interpreted as a free tryptophan. The
figure was prepared with DINO (Phillipsen, 1998).
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Figure 6.
Figure 6 Proposed scheme of the effect of calcium on
membrane-clustered E-cadherin. Low Ca^2+ concentrations
stabilize the rod-like structure (A and B), medium and high
concentrations result in cis-dimerization (C) and Trp2 docking
in its hydrophobic cavity which enables trans-interaction (D).
Domains 1–5 are drawn as gray blocks, with the hydrophobic
cavity to which Trp2 binds in domain 1. Trp2 is shown as a green
symbol with the A-strand
as a connecting black line. Bound Ca^2+ ions are symbolized by
circles and the different K[d] values of the distinct binding
sites by different colors: blue, 30  M;
red, 330 M;
yellow, 2 mM.
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The above figures are
reprinted
from an Open Access publication published by Macmillan Publishers Ltd:
EMBO J
(1999,
18,
1738-1747)
copyright 1999.
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Figures were
selected
by an automated process.
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Literature references that cite this PDB file's key reference
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PubMed id
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Reference
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J.Vendome,
S.Posy,
X.Jin,
F.Bahna,
G.Ahlsen,
L.Shapiro,
and
B.Honig
(2011).
Molecular design principles underlying β-strand swapping in the adhesive dimerization of cadherins.
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Nat Struct Mol Biol,
18,
693-700.
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PDB code:
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K.Gehmlich,
P.Syrris,
E.Peskett,
A.Evans,
E.Ehler,
A.Asimaki,
A.Anastasakis,
A.Tsatsopoulou,
A.I.Vouliotis,
C.Stefanadis,
J.E.Saffitz,
N.Protonotarios,
and
W.J.McKenna
(2011).
Mechanistic insights into arrhythmogenic right ventricular cardiomyopathy caused by desmocollin-2 mutations.
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Cardiovasc Res,
90,
77-87.
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L.Mohamet,
K.Hawkins,
and
C.M.Ward
(2011).
Loss of function of e-cadherin in embryonic stem cells and the relevance to models of tumorigenesis.
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J Oncol,
2011,
352616.
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R.L.Dusek,
and
L.D.Attardi
(2011).
Desmosomes: new perpetrators in tumour suppression.
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Nat Rev Cancer,
11,
317-323.
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S.Hong,
R.B.Troyanovsky,
and
S.M.Troyanovsky
(2011).
Cadherin exits the junction by switching its adhesive bond.
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J Cell Biol,
192,
1073-1083.
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A.Pertsinidis,
Y.Zhang,
and
S.Chu
(2010).
Subnanometre single-molecule localization, registration and distance measurements.
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Nature,
466,
647-651.
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C.Ciatto,
F.Bahna,
N.Zampieri,
H.C.VanSteenhouse,
P.S.Katsamba,
G.Ahlsen,
O.J.Harrison,
J.Brasch,
X.Jin,
S.Posy,
J.Vendome,
B.Ranscht,
T.M.Jessell,
B.Honig,
and
L.Shapiro
(2010).
T-cadherin structures reveal a novel adhesive binding mechanism.
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Nat Struct Mol Biol,
17,
339-347.
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PDB codes:
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E.A.Barnes,
H.L.Kenerson,
X.Jiang,
and
R.S.Yeung
(2010).
Tuberin regulates E-cadherin localization: implications in epithelial-mesenchymal transition.
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Am J Pathol,
177,
1765-1778.
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G.R.Owen,
and
D.L.Stokes
(2010).
Exploring the Nature of Desmosomal Cadherin Associations in 3D.
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Dermatol Res Pract,
2010,
930401.
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H.M.Elledge,
P.Kazmierczak,
P.Clark,
J.S.Joseph,
A.Kolatkar,
P.Kuhn,
and
U.Müller
(2010).
Structure of the N terminus of cadherin 23 reveals a new adhesion mechanism for a subset of cadherin superfamily members.
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Proc Natl Acad Sci U S A,
107,
10708-10712.
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PDB code:
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M.Fernández-Monreal,
T.Oung,
H.H.Hanson,
R.O'Leary,
W.G.Janssen,
G.Dolios,
R.Wang,
and
G.R.Phillips
(2010).
Gamma-protocadherins are enriched and transported in specialized vesicles associated with the secretory pathway in neurons.
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Eur J Neurosci,
32,
921-931.
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M.Sotomayor,
W.A.Weihofen,
R.Gaudet,
and
D.P.Corey
(2010).
Structural determinants of cadherin-23 function in hearing and deafness.
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Neuron,
66,
85.
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PDB codes:
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O.J.Harrison,
F.Bahna,
P.S.Katsamba,
X.Jin,
J.Brasch,
J.Vendome,
G.Ahlsen,
K.J.Carroll,
S.R.Price,
B.Honig,
and
L.Shapiro
(2010).
Two-step adhesive binding by classical cadherins.
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Nat Struct Mol Biol,
17,
348-357.
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PDB codes:
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Q.le Duc,
Q.Shi,
I.Blonk,
A.Sonnenberg,
N.Wang,
D.Leckband,
and
J.de Rooij
(2010).
Vinculin potentiates E-cadherin mechanosensing and is recruited to actin-anchored sites within adherens junctions in a myosin II-dependent manner.
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J Cell Biol,
189,
1107-1115.
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A.T.Dawes
(2009).
A mathematical model of alpha-catenin dimerization at adherens junctions in polarized epithelial cells.
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J Theor Biol,
257,
480-488.
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D.Osumi,
M.Takahashi,
E.Miyoshi,
S.Yokoe,
S.H.Lee,
K.Noda,
S.Nakamori,
J.Gu,
Y.Ikeda,
Y.Kuroki,
K.Sengoku,
M.Ishikawa,
and
N.Taniguchi
(2009).
Core fucosylation of E-cadherin enhances cell-cell adhesion in human colon carcinoma WiDr cells.
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Cancer Sci,
100,
888-895.
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H.B.Guo,
H.Johnson,
M.Randolph,
and
M.Pierce
(2009).
Regulation of homotypic cell-cell adhesion by branched N-glycosylation of N-cadherin extracellular EC2 and EC3 domains.
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J Biol Chem,
284,
34986-34997.
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K.Zheng,
J.S.Laurence,
K.Kuczera,
G.Verkhivker,
C.R.Middaugh,
and
T.J.Siahaan
(2009).
Characterization of multiple stable conformers of the EC5 domain of E-cadherin and the interaction of EC5 with E-cadherin peptides.
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Chem Biol Drug Des,
73,
584-598.
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L.Shapiro,
and
W.I.Weis
(2009).
Structure and biochemistry of cadherins and catenins.
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Cold Spring Harbor Perspect Biol,
1,
a003053.
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M.Trivedi,
R.A.Davis,
Y.Shabaik,
A.Roy,
G.Verkhivker,
J.S.Laurence,
C.R.Middaugh,
and
T.J.Siahaan
(2009).
The role of covalent dimerization on the physical and chemical stability of the EC1 domain of human E-cadherin.
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J Pharm Sci,
98,
3562-3574.
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P.Hulpiau,
and
F.van Roy
(2009).
Molecular evolution of the cadherin superfamily.
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Int J Biochem Cell Biol,
41,
349-369.
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Y.Huang,
Y.Zhou,
A.Castiblanco,
W.Yang,
E.M.Brown,
and
J.J.Yang
(2009).
Multiple Ca(2+)-binding sites in the extracellular domain of the Ca(2+)-sensing receptor corresponding to cooperative Ca(2+) response.
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Biochemistry,
48,
388-398.
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Y.Li,
M.Hofmann,
Q.Wang,
L.Teng,
L.K.Chlewicki,
H.Pircher,
and
R.A.Mariuzza
(2009).
Structure of natural killer cell receptor KLRG1 bound to E-cadherin reveals basis for MHC-independent missing self recognition.
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Immunity,
31,
35-46.
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PDB codes:
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Y.Zhang,
S.Sivasankar,
W.J.Nelson,
and
S.Chu
(2009).
Resolving cadherin interactions and binding cooperativity at the single-molecule level.
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Proc Natl Acad Sci U S A,
106,
109-114.
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C.B.Lira,
K.Chu,
Y.C.Lee,
M.C.Hu,
and
S.H.Lin
(2008).
Expression of the extracellular domain of OB-cadherin as an Fc fusion protein using bicistronic retroviral expression vector.
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Protein Expr Purif,
61,
220-226.
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C.Y.Tai,
S.A.Kim,
and
E.M.Schuman
(2008).
Cadherins and synaptic plasticity.
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Curr Opin Cell Biol,
20,
567-575.
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D.Studer,
B.M.Humbel,
and
M.Chiquet
(2008).
Electron microscopy of high pressure frozen samples: bridging the gap between cellular ultrastructure and atomic resolution.
|
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Histochem Cell Biol,
130,
877-889.
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G.M.Pitari,
J.E.Lin,
F.J.Shah,
W.J.Lubbe,
D.S.Zuzga,
P.Li,
S.Schulz,
and
S.A.Waldman
(2008).
Enterotoxin preconditioning restores calcium-sensing receptor-mediated cytostasis in colon cancer cells.
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Carcinogenesis,
29,
1601-1607.
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J.Waschke
(2008).
The desmosome and pemphigus.
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Histochem Cell Biol,
130,
21-54.
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M.P.Stemmler
(2008).
Cadherins in development and cancer.
|
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Mol Biosyst,
4,
835-850.
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M.Sotomayor,
and
K.Schulten
(2008).
The allosteric role of the Ca2+ switch in adhesion and elasticity of C-cadherin.
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Biophys J,
94,
4621-4633.
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Q.Shi,
Y.H.Chien,
and
D.Leckband
(2008).
Biophysical properties of cadherin bonds do not predict cell sorting.
|
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J Biol Chem,
283,
28454-28463.
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S.A.Dames,
E.Bang,
D.Haüssinger,
T.Ahrens,
J.Engel,
and
S.Grzesiek
(2008).
Insights into the Low Adhesive Capacity of Human T-cadherin from the NMR Structure of Its N-terminal Extracellular Domain.
|
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J Biol Chem,
283,
23485-23495.
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PDB code:
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S.Posy,
L.Shapiro,
and
B.Honig
(2008).
Sequence and structural determinants of strand swapping in cadherin domains: do all cadherins bind through the same adhesive interface?
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J Mol Biol,
378,
954-968.
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Y.H.Chien,
N.Jiang,
F.Li,
F.Zhang,
C.Zhu,
and
D.Leckband
(2008).
Two stage cadherin kinetics require multiple extracellular domains but not the cytoplasmic region.
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J Biol Chem,
283,
1848-1856.
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A.Al-Amoudi,
D.C.Díez,
M.J.Betts,
and
A.S.Frangakis
(2007).
The molecular architecture of cadherins in native epidermal desmosomes.
|
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Nature,
450,
832-837.
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A.Aquilina-Beck,
K.Ilagan,
Q.Liu,
and
J.O.Liang
(2007).
Nodal signaling is required for closure of the anterior neural tube in zebrafish.
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BMC Dev Biol,
7,
126.
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E.Parisini,
J.M.Higgins,
J.H.Liu,
M.B.Brenner,
and
J.H.Wang
(2007).
The crystal structure of human E-cadherin domains 1 and 2, and comparison with other cadherins in the context of adhesion mechanism.
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J Mol Biol,
373,
401-411.
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PDB code:
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H.Tsuiji,
L.Xu,
K.Schwartz,
and
B.M.Gumbiner
(2007).
Cadherin conformations associated with dimerization and adhesion.
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J Biol Chem,
282,
12871-12882.
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J.Waschke,
C.Menendez-Castro,
P.Bruggeman,
R.Koob,
M.Amagai,
H.J.Gruber,
D.Drenckhahn,
and
W.Baumgartner
(2007).
Imaging and force spectroscopy on desmoglein 1 using atomic force microscopy reveal multivalent Ca(2+)-dependent, low-affinity trans-interaction.
|
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J Membr Biol,
216,
83-92.
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K.Nag,
and
G.M.Watson
(2007).
Repair of hair cells following mild trauma may involve extracellular chaperones.
|
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J Comp Physiol A Neuroethol Sens Neural Behav Physiol,
193,
1045-1053.
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L.Saglietti,
C.Dequidt,
K.Kamieniarz,
M.C.Rousset,
P.Valnegri,
O.Thoumine,
F.Beretta,
L.Fagni,
D.Choquet,
C.Sala,
M.Sheng,
and
M.Passafaro
(2007).
Extracellular interactions between GluR2 and N-cadherin in spine regulation.
|
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Neuron,
54,
461-477.
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L.Shapiro,
J.Love,
and
D.R.Colman
(2007).
Adhesion molecules in the nervous system: structural insights into function and diversity.
|
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Annu Rev Neurosci,
30,
451-474.
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M.J.Harrington,
E.Hong,
O.Fasanmi,
and
R.Brewster
(2007).
Cadherin-mediated adhesion regulates posterior body formation.
|
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BMC Dev Biol,
7,
130.
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Q.Liu,
R.A.Frey,
S.G.Babb-Clendenon,
B.Liu,
J.Francl,
A.L.Wilson,
J.A.Marrs,
and
D.L.Stenkamp
(2007).
Differential expression of photoreceptor-specific genes in the retina of a zebrafish cadherin2 mutant glass onion and zebrafish cadherin4 morphants.
|
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Exp Eye Res,
84,
163-175.
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R.B.Troyanovsky,
O.Laur,
and
S.M.Troyanovsky
(2007).
Stable and unstable cadherin dimers: mechanisms of formation and roles in cell adhesion.
|
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Mol Biol Cell,
18,
4343-4352.
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S.Pokutta,
and
W.I.Weis
(2007).
Structure and mechanism of cadherins and catenins in cell-cell contacts.
|
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Annu Rev Cell Dev Biol,
23,
237-261.
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S.von der Hardt,
J.Bakkers,
A.Inbal,
L.Carvalho,
L.Solnica-Krezel,
C.P.Heisenberg,
and
M.Hammerschmidt
(2007).
The Bmp gradient of the zebrafish gastrula guides migrating lateral cells by regulating cell-cell adhesion.
|
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Curr Biol,
17,
475-487.
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X.Chen,
C.Molino,
L.Liu,
and
B.M.Gumbiner
(2007).
Structural elements necessary for oligomerization, trafficking, and cell sorting function of paraxial protocadherin.
|
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J Biol Chem,
282,
32128-32137.
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X.Chen,
T.D.Kim,
C.V.Carman,
L.Z.Mi,
G.Song,
and
T.A.Springer
(2007).
Structural plasticity in Ig superfamily domain 4 of ICAM-1 mediates cell surface dimerization.
|
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Proc Natl Acad Sci U S A,
104,
15358-15363.
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PDB code:
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A.K.Prakasam,
V.Maruthamuthu,
and
D.E.Leckband
(2006).
Similarities between heterophilic and homophilic cadherin adhesion.
|
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Proc Natl Acad Sci U S A,
103,
15434-15439.
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A.Liwosz,
T.Lei,
and
M.A.Kukuruzinska
(2006).
N-glycosylation affects the molecular organization and stability of E-cadherin junctions.
|
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J Biol Chem,
281,
23138-23149.
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A.Prasad,
H.Zhao,
J.M.Rutherford,
N.Housley,
C.Nichols,
and
S.Pedigo
(2006).
Effect of linker segments on the stability of epithelial cadherin Domain 2.
|
| |
Proteins,
62,
111-121.
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D.Leckband,
and
A.Prakasam
(2006).
Mechanism and dynamics of cadherin adhesion.
|
| |
Annu Rev Biomed Eng,
8,
259-287.
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F.Cailliez,
and
R.Lavery
(2006).
Dynamics and stability of E-cadherin dimers.
|
| |
Biophys J,
91,
3964-3971.
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H.Morishita,
M.Umitsu,
Y.Murata,
N.Shibata,
K.Udaka,
Y.Higuchi,
H.Akutsu,
T.Yamaguchi,
T.Yagi,
and
T.Ikegami
(2006).
Structure of the cadherin-related neuronal receptor/protocadherin-alpha first extracellular cadherin domain reveals diversity across cadherin families.
|
| |
J Biol Chem,
281,
33650-33663.
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Cell,
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PDB codes:
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Y.S.Chu,
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Nat Struct Mol Biol,
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PDB codes:
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A.Shimizu,
A.Ishiko,
T.Ota,
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In vivo ultrastructural localization of the desmoglein 3 adhesive interface to the desmosome mid-line.
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Structure,
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PDB code:
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D.Häussinger,
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Cell Motil Cytoskeleton,
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J Biol Chem,
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Ann N Y Acad Sci,
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Regulation of desmosome assembly and adhesion.
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The minimal essential unit for cadherin-mediated intercellular adhesion comprises extracellular domains 1 and 2.
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J Biol Chem,
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MuSC is involved in regulating axonal fasciculation of mouse primary vestibular afferents.
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Adhesive and lateral E-cadherin dimers are mediated by the same interface.
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Mol Cell Biol,
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Untangling desmosomal knots with electron tomography.
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Science,
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PDB codes:
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Y.Hanakawa,
T.Selwood,
D.Woo,
C.Lin,
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Calcium-dependent conformation of desmoglein 1 is required for its cleavage by exfoliative toxin.
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J Invest Dermatol,
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Structure,
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Cancer Invest,
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Fast dissociation kinetics between individual E-cadherin fragments revealed by flow chamber analysis.
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EMBO J,
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Disulfide bond formation promotes the cis- and trans-dimerization of the E-cadherin-derived first repeat.
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J Biol Chem,
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Dynamic interplay between adhesive and lateral E-cadherin dimers.
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Mol Cell Biol,
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Dynamics of ligand-induced, Rac1-dependent anchoring of cadherins to the actin cytoskeleton.
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J Cell Biol,
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Lateral dimerization of the E-cadherin extracellular domain is necessary but not sufficient for adhesive activity.
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J Biol Chem,
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Synergy between extracellular modules of vascular endothelial cadherin promotes homotypic hexameric interactions.
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J Biol Chem,
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J Biol Chem,
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B.M.Gumbiner,
and
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C-cadherin ectodomain structure and implications for cell adhesion mechanisms.
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Science,
296,
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PDB code:
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W.C.Prozialeck,
M.J.Fay,
P.C.Lamar,
C.A.Pearson,
I.Sigar,
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Chlamydia trachomatis disrupts N-cadherin-dependent cell-cell junctions and sequesters beta-catenin in human cervical epithelial cells.
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Infect Immun,
70,
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W.D.Schubert,
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Structure of internalin, a major invasion protein of Listeria monocytogenes, in complex with its human receptor E-cadherin.
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Cell,
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PDB codes:
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|
Y.Hanakawa,
N.M.Schechter,
C.Lin,
L.Garza,
H.Li,
T.Yamaguchi,
Y.Fudaba,
K.Nishifuji,
M.Sugai,
M.Amagai,
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(2002).
Molecular mechanisms of blister formation in bullous impetigo and staphylococcal scalded skin syndrome.
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J Clin Invest,
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The sequence determinants of cadherin molecules.
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Protein Sci,
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X-ray structure of junctional adhesion molecule: structural basis for homophilic adhesion via a novel dimerization motif.
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EMBO J,
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PDB code:
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R.Iino,
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Single molecule imaging of green fluorescent proteins in living cells: E-cadherin forms oligomers on the free cell surface.
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Biophys J,
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S.Chappuis-Flament,
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Multiple cadherin extracellular repeats mediate homophilic binding and adhesion.
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J Cell Biol,
154,
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Direct measurements of multiple adhesive alignments and unbinding trajectories between cadherin extracellular domains.
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Biophys J,
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Curr Opin Cell Biol,
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D.Logeart,
S.N.Hatem,
C.Rücker-Martin,
N.Chossat,
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Highly efficient adenovirus-mediated gene transfer to cardiac myocytes after single-pass coronary delivery.
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J Pathol,
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A novel family of cyclic peptide antagonists suggests that N-cadherin specificity is determined by amino acids that flank the HAV motif.
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J Biol Chem,
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Trimerization of cell adhesion molecule L1 mimics clustered L1 expression on the cell surface: influence on L1-ligand interactions and on promotion of neurite outgrowth.
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J Neurochem,
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The crystal structure of the ligand binding module of axonin-1/TAG-1 suggests a zipper mechanism for neural cell adhesion.
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| |
Cell,
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PDB code:
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M.C.Deller,
and
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Cell surface receptors.
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Homophilic adhesion by cadherins.
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The most recent references are shown first.
Citation data come partly from CiteXplore and partly
from an automated harvesting procedure. Note that this is likely to be
only a partial list as not all journals are covered by
either method. However, we are continually building up the citation data
so more and more references will be included with time.
Where a reference describes a PDB structure, the PDB
code is
shown on the right.
|
|
Links
